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Molecular Analytical Robotics Assays

Deliverables

4D-model of DNA pore

Upon assembly of a functional DNA pore, which is verified to insert itself in biological membrane environments, the pore will be analysed using electron cryo-tomography. Subsequently, 4D-models will be created.

4D-model of archaellum

Upon expression, purification and biochemical analysis of several wildtype and mutated archaellum subunits, the proteins will be analysed using electron cryo-microscopy. We will use the archaellum proteins from different archaea such as S. acidocaldarius, P.furiosus, M. jannaschii and Archaeoglobus fulgidus. We will also image the intact archaellar motor in situ in Haloferax volcanii cells. It is expected this variety of model organisms will ensure that structural information can be obtained. Subsequently, 4D-models will be created: a description of the mechanism that accounts for function.

DNA origami design software

Based on existing DNA origami design software, a novel bioinformatic toolkit will be created to enable the automated protein embedding function into the DNA scaffold using the 4D models from WP3

Collaborative website

A website that will facilitate internal and external communication and dissemination.

Data management plan

A Data Management Plan will be elaborated within the first six months of the project, guaranteeing an appropriate disclosure of research data to the public and standardised data management within the project. The types of data that will be generated and collected within the project comprise design data (oligonucleotide sequences, technical drawings, etc.), laboratory test data (images, reaction parameters, etc.), software and metadata (final results/scientific insights, documentation, reports, publications, etc.). Three different levels of confidentiality will be defined according to IP issues and marketing strategies: classified data, IPR relevant data and public data.

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Publications

Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius

Author(s): Lena Hoffmann, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid, Sonja-V. Albers
Published in: MicrobiologyOpen, Issue 6/1, 2017, Page(s) e00414, ISSN 2045-8827
DOI: 10.1002/mbo3.414

(Poly)cation-induced protection of conventional and wireframe DNA origami nanostructures

Author(s): Yasaman Ahmadi, Elisa De Llano, Ivan Barišić
Published in: Nanoscale, Issue 10/16, 2018, Page(s) 7494-7504, ISSN 2040-3364
DOI: 10.1039/C7NR09461B

ArnS, a kinase involved in starvation-induced archaellum expression

Author(s): M. Florencia Haurat, Ana Sofia Figueiredo, Lena Hoffmann, Lingling Li, Katharina Herr, Amanda J. Wilson, Morgan Beeby, Jörg Schaber, Sonja-Verena Albers
Published in: Molecular Microbiology, Issue 103/1, 2017, Page(s) 181-194, ISSN 0950-382X
DOI: 10.1111/mmi.13550

Multiscale Visualization and Scale-Adaptive Modification of DNA Nanostructures

Author(s): Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, M. Eduard Groller, Ivan Barisic, Ivan Viola
Published in: IEEE Transactions on Visualization and Computer Graphics, Issue 24/1, 2018, Page(s) 1014-1024, ISSN 1077-2626
DOI: 10.1109/TVCG.2017.2743981

DimSUM: Dimension and Scale Unifying Map for Visual Abstraction of DNA Origami Structures

Author(s): H. Miao, E. De Llano, T. Isenberg, M. E. Gröller, I. Barišić, I. Viola
Published in: Computer Graphics Forum, Issue 37/3, 2018, Page(s) 403-413, ISSN 0167-7055
DOI: 10.1111/cgf.13429